Alignments for a candidate for treC in Cronobacter condimenti 1330

GapMind for catabolism of small carbon sources

Alignments for a candidate for treC in Cronobacter condimenti 1330

Align trehalose-6-phosphate hydrolase (TreA;BSU07810) (EC 3.2.1.93) (characterized)
to candidate WP_007665537.1 BN137_RS16145 alpha-glucosidase

Query= CAZy::CAB12610.1
         (561 letters)



>NCBI__GCF_000319285.1:WP_007665537.1
          Length = 551

 Score =  565 bits (1457), Expect = e-165
 Identities = 269/554 (48%), Positives = 364/554 (65%), Gaps = 14/554 (2%)

Query: 1   MKTEQTPWWKKAVVYQIYPKSFNDTTGNGVGDLNGIIEKLDYLKTLQVDVLWLTPIYDSP 60
           MK     WW  AVVYQIYP+SF D  G+GVGDL GII KLDYL+ L ++++WL+P+Y SP
Sbjct: 1   MKAIDKKWWHNAVVYQIYPRSFMDANGDGVGDLAGIISKLDYLQQLGINLIWLSPVYKSP 60

Query: 61  QHDNGYDIRDYYSIYPEYGTMEDFERLVSEAHKRDLKVVMDLVVNHTSTEHKWFREAISS 120
             DNGYDI DY  I  E+GTM + E+L++EA  R++ ++MDLVVNHTS EH WF EA   
Sbjct: 61  MDDNGYDISDYDDIAAEFGTMAEMEQLITEAKARNIYILMDLVVNHTSDEHPWFLEAKKG 120

Query: 121 IDSPYRDFYIWKKPQENGSVPTNWESKFGGSAWELDEASGQYYLHLFDVTQADLNWENEE 180
            D+PYR+FYIW+KP  +G  P ++ S FGGS W  DEASG+YYLH F V Q DLNWEN  
Sbjct: 121 KDNPYREFYIWRKPAPDGGPPNDYRSHFGGSGWAYDEASGEYYLHQFSVRQPDLNWENPR 180

Query: 181 VRKHVYDMMHFWFEKGIDGFRLDVINLISKDQRFPNAEEGDGRSFYTDGPRVHEFLHEMN 240
           V++ ++ MM+ W +KGI GFR+DVI+LI K+           R    +G  +H  L +MN
Sbjct: 181 VQEEIHAMMNRWLDKGIGGFRMDVIDLIGKEV---------DRQIMANGKHLHVLLRQMN 231

Query: 241 EKVFSHYDSMTVGEMSSTTVDHCIRYTNPDNKELDMTFSFHHLKVDY-PNGEKWALAPFD 299
              F   DS+TVGE  S T +  + Y++P+ +EL M F F H+K  +     KW   PFD
Sbjct: 232 AATFGPRDSLTVGEAWSATPEDALLYSDPERQELSMVFQFEHIKQTWDEKAGKWRSRPFD 291

Query: 300 FLKLKEILSDWQTGMHAGGGWNALFWCNHDQPRVVSRYGDDGAYRVKSAKMLATAIHMMQ 359
             + K ++  WQT + A  GWN+LFW NHD PR VS++G+DG +R  SAKMLATA+H ++
Sbjct: 292 LPRFKAVIDKWQTAL-ADRGWNSLFWSNHDLPRAVSKFGNDGEFREVSAKMLATALHCLR 350

Query: 360 GTPYIYQGEELGMTNPKFTDISSYRDVESLNMYHAFKEKGMADQDITAILQAKSRDNSRT 419
           GTPYIYQGEE+GMTN +++ I  YRD+ESLN Y      G+   ++   + A  RDN+RT
Sbjct: 351 GTPYIYQGEEIGMTNVRYSTIEEYRDIESLNFYRELIAGGLTHDEMMTGIYANGRDNART 410

Query: 420 PVQWDATENGGFTTGTPWIPVAGNYREINAEAALRDQNSVFYHYQKLIQIRKMYDIVTEG 479
           P+QWD + N GFTTG PW+ V  NYR+IN   AL + +S+ +HYQKL+ +RK + I+  G
Sbjct: 411 PMQWDDSPNSGFTTGMPWLGVNPNYRDINVAQALAEPDSILWHYQKLVALRKQHPILVYG 470

Query: 480 TYEIIAKDDPNIFAYLRHGSNEKLLVINNFYGTEAAFTLPDSLAPDEWKAEVLLTNDEAR 539
            Y+++  + P IFA++R    + LLV+NNF+G     TLP   A   W  E L++N   R
Sbjct: 471 DYQMLFAEHPEIFAWVRRYEGDTLLVVNNFFGNH--ITLPVPEAMQAWHGECLISNYAPR 528

Query: 540 EGLQ-NMTLRPYES 552
           + L  ++ L+PYES
Sbjct: 529 DQLAVSLELQPYES 542


Lambda     K      H
   0.318    0.135    0.423 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1121
Number of extensions: 58
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 561
Length of database: 551
Length adjustment: 36
Effective length of query: 525
Effective length of database: 515
Effective search space:   270375
Effective search space used:   270375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources